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root/OpenMD/branches/development/src/brains/DataStorage.hpp

Comparing:
trunk/src/brains/DataStorage.hpp (file contents), Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
branches/development/src/brains/DataStorage.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 53 | Line 54
54		#include <math/Vector3.hpp>
55		#include <math/SquareMatrix3.hpp>
56
57	<	namespace oopse {
57	>	namespace OpenMD {
58	>	/**
59	>	* @class DataStorage
60	>	* @warning do not try to insert element into (or ease element from) private member data
61	>	* of DataStorage directly.
62	>	* @todo DataStorage may need refactoring. Every vector can inherit from the same base class
63	>	* which will make it easy to maintain
64	>	*/
65	>	class DataStorage {
66	>	public:
67	>
68	>	enum{
69	>	dslPosition = 1,
70	>	dslVelocity = 2,
71	>	dslAmat = 4,
72	>	dslAngularMomentum = 8,
73	>	dslElectroFrame = 16,
74	>	dslZAngle = 32,
75	>	dslForce = 64,
76	>	dslTorque = 128,
77	>	dslParticlePot = 256,
78	>	dslDensity = 512,
79	>	dslFunctional = 1024,
80	>	dslFunctionalDerivative = 2048,
81	>	dslElectricField = 4096,
82	>	dslSkippedCharge = 8192
83	>	};
84	>
85	>	DataStorage();
86	>	DataStorage(int size, int storageLayout = 16383);
87	>	/** return the size of this DataStorage. */
88	>	int getSize();
89		/**
90	<	* @class DataStorage
91	<	* @warning do not try to insert element into (or ease element from) private member data
60	<	* of DataStorage directly.
61	<	* @todo DataStorage may need refactorying. Every std::vector can inherit from the same base class
62	<	* which will make it easy to maintain
90	>	* Changes the size of this DataStorage.
91	>	* @param size new size of this DataStorage
92		*/
93	<	class DataStorage {
94	<	public:
93	>	void resize(int newSize);
94	>	/**
95	>	* Reallocates memory manually.
96	>	*
97	>	* The main reason for using reserve() is efficiency if you know
98	>	* the capacity to which your vector must eventually grow,
99	>	* then it is usually more efficient to allocate that memory all
100	>	* at once.
101	>	*/
102	>	void reserve(int size);
103	>	/**
104	>	* Copies data inside DataStorage class.
105	>	*
106	>	* Copy function actually call copy for every vector in
107	>	* DataStorage class.  One Precondition of copy is that
108	>	* target is not within the range [source, soruce + num]
109	>	*
110	>	* @param souce
111	>	* @param num number of element to be moved
112	>	* @param target
113	>	*/
114	>	void copy(int source, int num, int target);
115	>	/** Returns the storage layout  */
116	>	int getStorageLayout();
117	>	/** Sets the storage layout  */
118	>	void setStorageLayout(int layout);
119	>	/** Returns the pointer of internal array */
120	>	RealType *getArrayPointer(int whichArray);
121
122	<	enum{
123	<	dslPosition = 1,
124	<	dslVelocity = 2,
125	<	dslAmat = 4,
126	<	dslAngularMomentum = 8,
127	<	dslElectroFrame = 16,
128	<	dslZAngle = 32,
129	<	dslForce = 64,
130	<	dslTorque = 128
131	<	};
122	>	std::vector<Vector3d> position;        /** position array */
123	>	std::vector<Vector3d> velocity;        /** velocity array */
124	>	std::vector<RotMat3x3d> aMat;          /** rotation matrix array */
125	>	std::vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
126	>	std::vector<Mat3x3d> electroFrame;     /** the lab frame unit std::vector array*/
127	>	std::vector<RealType> zAngle;          /** z-angle array */
128	>	std::vector<Vector3d> force;           /** force array */
129	>	std::vector<Vector3d> torque;          /** torque array */
130	>	std::vector<RealType> particlePot;     /** particle potential arrray */
131	>	std::vector<RealType> density;         /** electron density */
132	>	std::vector<RealType> functional;      /** density functional */
133	>	std::vector<RealType> functionalDerivative; /** derivative of functional */
134	>	std::vector<Vector3d> electricField;   /** local electric field */
135	>	std::vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */
136
137	+	static int getBytesPerStuntDouble(int layout);
138
139	<	DataStorage();
80	<	DataStorage(int size, int storageLayout = 255);
81	<	/** return the size of this DataStorage. */
82	<	int getSize();
83	<	/**
84	<	* Changes the size of this DataStorage.
85	<	* @param size new size of this DataStorage
86	<	*/
87	<	void resize(int newSize);
88	<	/**
89	<	* Reallocates memory manually. The main reason for using reserve() is efficiency
90	<	* if you know the capacity to which your std::vector must eventually grow, then it is usually more
91	<	* efficient to allocate that memory all at once.
92	<	*/
93	<	void reserve(int size);
94	<	/**
95	<	* Copies data inside DataStorage class.
96	<	* Copy function actually call std::copy for every std::vector in DataStorage class.
97	<	* One Precondition of std::copy is that target is not within the range [soruce, soruce + num]
98	<	* @param souce
99	<	* @param num number of element to be moved
100	<	* @param target
101	<	*/
102	<	void copy(int source, int num, int target);
103	<	/** Returns the storage layout  */
104	<	int getStorageLayout();
105	<	/** Sets the storage layout  */
106	<	void setStorageLayout(int layout);
107	<	/** Returns the pointer of internal array */
108	<	double *getArrayPointer(int whichArray);
139	>	private:
140
141	<	std::vector<Vector3d> position;               /** position array */
142	<	std::vector<Vector3d> velocity;               /** velocity array */
143	<	std::vector<RotMat3x3d> aMat;            /** rotation matrix array */
113	<	std::vector<Vector3d> angularMomentum;/** angular momentum array (body-fixed) */
114	<	std::vector<Mat3x3d> electroFrame;                /** the lab frame unit std::vector array*/
115	<	std::vector<double> zAngle;              /** z -angle array */
116	<	std::vector<Vector3d> force;               /** force array */
117	<	std::vector<Vector3d> torque;               /** torque array */
141	>	RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
142	>	RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
143	>	RealType* internalGetArrayPointer(std::vector<RealType>& v);
144
119	–	static int getBytesPerStuntDouble(int layout);
120	–
121	–	private:
122	–
123	–	double* internalGetArrayPointer(std::vector<Vector3d>& v);
145
146	<	double* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
147	<	double* internalGetArrayPointer(std::vector<double>& v);
127	<
128	<	template<typename T>
129	<	void internalResize(std::vector<T>& v, int newSize);
146	>	template<typename T>
147	>	void internalResize(std::vector<T>& v, int newSize);
148
149	<	template<typename T>
150	<	void internalCopy(std::vector<T>& v, int source,  int num, int target);
149	>	template<typename T>
150	>	void internalCopy(std::vector<T>& v, int source,  int num, int target);
151
152	<	int size_;
153	<	int storageLayout_;
152	>	int size_;
153	>	int storageLayout_;
154
155	<	};
155	>	};
156
157		}
158		#endif //BRAINS_DATASTORAGE_HPP

Comparing:
trunk/src/brains/DataStorage.hpp (property svn:keywords), Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
branches/development/src/brains/DataStorage.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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